X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSequenceRenderer.java;h=feb2705ab03b2e711cd192a4a258d8697377ac31;hb=be32c14cd8e48fe0a207cd7030cb9cd46f894678;hp=b048e91cd3fa12999c0832fbec758933079505b3;hpb=28a4f823a8d3e6eae1a4569d8022c5a20fd0e3c7;p=jalview.git diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java index b048e91..feb2705 100755 --- a/src/jalview/appletgui/SequenceRenderer.java +++ b/src/jalview/appletgui/SequenceRenderer.java @@ -1,23 +1,26 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8) - * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * * Jalview is free software: you can redistribute it and/or * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. * * Jalview is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of MERCHANTABILITY or FITNESS FOR A PARTICULAR * PURPOSE. See the GNU General Public License for more details. * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.appletgui; -import jalview.datamodel.AlignmentAnnotation; +import jalview.api.FeatureRenderer; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.schemes.ColourSchemeI; @@ -83,6 +86,31 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer return resBoxColour; } + /** + * Get the residue colour at the given sequence position - as determined by + * the sequence group colour (if any), else the colour scheme, possibly + * overridden by a feature colour. + * + * @param seq + * @param position + * @param fr + * @return + */ + @Override + public Color getResidueColour(final SequenceI seq, int position, + FeatureRenderer fr) + { + // TODO replace 8 or so code duplications with calls to this method + // (refactored as needed) + Color col = getResidueBoxColour(seq, position); + + if (fr != null) + { + col = fr.findFeatureColour(col, seq, position); + } + return col; + } + void getBoxColour(ColourSchemeI cs, SequenceI seq, int i) { if (cs != null) @@ -132,7 +160,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer int length = seq.getLength(); int curStart = -1; - int curWidth = av.charWidth; + int curWidth = av.getCharWidth(), avCharWidth = av.getCharWidth(), avCharHeight = av + .getCharHeight(); Color tempColour = null; while (i <= end) @@ -157,40 +186,41 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer { if (tempColour != null) { - graphics.fillRect(av.charWidth * (curStart - start), y1, - curWidth, av.charHeight); + graphics.fillRect(avCharWidth * (curStart - start), y1, curWidth, + avCharHeight); } graphics.setColor(resBoxColour); curStart = i; - curWidth = av.charWidth; + curWidth = avCharWidth; tempColour = resBoxColour; } else { - curWidth += av.charWidth; + curWidth += avCharWidth; } i++; } - graphics.fillRect(av.charWidth * (curStart - start), y1, curWidth, - av.charHeight); + graphics.fillRect(avCharWidth * (curStart - start), y1, curWidth, + avCharHeight); } public void drawText(SequenceI seq, int start, int end, int y1) { + int avCharWidth = av.getCharWidth(), avCharHeight = av.getCharHeight(); Font boldFont = null; boolean bold = false; - if (av.upperCasebold) + if (av.isUpperCasebold()) { - boldFont = new Font(av.getFont().getName(), Font.BOLD, av.charHeight); + boldFont = new Font(av.getFont().getName(), Font.BOLD, avCharHeight); graphics.setFont(av.getFont()); } - y1 += av.charHeight - av.charHeight / 5; // height/5 replaces pady + y1 += avCharHeight - avCharHeight / 5; // height/5 replaces pady int charOffset = 0; @@ -257,7 +287,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer } } - if (av.upperCasebold) + if (av.isUpperCasebold()) { fm = graphics.getFontMetrics(); if ('A' <= s && s <= 'Z') @@ -277,8 +307,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer } - charOffset = (av.charWidth - fm.charWidth(s)) / 2; - graphics.drawString(String.valueOf(s), charOffset + av.charWidth + charOffset = (avCharWidth - fm.charWidth(s)) / 2; + graphics.drawString(String.valueOf(s), charOffset + avCharWidth * (i - start), y1); } @@ -321,11 +351,11 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer public void drawHighlightedText(SequenceI seq, int start, int end, int x1, int y1) { - int pady = av.charHeight / 5; + int avCharWidth = av.getCharWidth(), avCharHeight = av.getCharHeight(); + int pady = avCharHeight / 5; int charOffset = 0; graphics.setColor(Color.black); - graphics.fillRect(x1, y1, av.charWidth * (end - start + 1), - av.charHeight); + graphics.fillRect(x1, y1, avCharWidth * (end - start + 1), avCharHeight); graphics.setColor(Color.white); char s = '~'; @@ -339,19 +369,19 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer s = seq.getCharAt(i); } - charOffset = (av.charWidth - fm.charWidth(s)) / 2; + charOffset = (avCharWidth - fm.charWidth(s)) / 2; graphics.drawString(String.valueOf(s), charOffset + x1 - + av.charWidth * (i - start), y1 + av.charHeight - pady); + + avCharWidth * (i - start), y1 + avCharHeight - pady); } } } public void drawCursor(SequenceI seq, int res, int x1, int y1) { - int pady = av.charHeight / 5; + int pady = av.getCharHeight() / 5; int charOffset = 0; graphics.setColor(Color.black); - graphics.fillRect(x1, y1, av.charWidth, av.charHeight); + graphics.fillRect(x1, y1, av.getCharWidth(), av.getCharHeight()); graphics.setColor(Color.white); graphics.setColor(Color.white); @@ -360,9 +390,9 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer if (av.validCharWidth) { - charOffset = (av.charWidth - fm.charWidth(s)) / 2; + charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2; graphics.drawString(String.valueOf(s), charOffset + x1, - (y1 + av.charHeight) - pady); + (y1 + av.getCharHeight()) - pady); } }